Genotype calling: Difference between revisions

Revision as of 18:38, 10 October 2012

The program can do genotype calling in different tempis.

output file .geno

-doGeno 32: , somewhat different dumps the binary posts for all samples, encoded as 3*nind double

The genotype are integers such that AA=0,AC=1,AG=2,AT=3,CC=4,CG=5,CT=6,GG=7,GT=8,TT=9

output is (-doGeno NOT 64) chr, pos, numberof samples times[ the above]

NB currently you also need to supply -doMaf to run this genotype calling

@@ Line 7: / Line 7: @@
 ;-doGeno 1:, print out major minor
-;-doGeno 2:, print the called genotype under HWE (suyeon maf prior method)
+;-doGeno 2:, print the called genotype as 0,1,2
-;-doGeno 4:, print out the genotype with the best raw likelihood
+;-doGeno 4:, print the called genotype as AA, AC, AG, ...
-;-doGeno 8:, print out the posteriour under the suyeon model
+;-doGeno 8:, print all 3 posts (major,major),(major,minor),(minor,minor)
-;-doGeno 16:, print all 3 posts (major,major),(major,minor),(minor,minor)
+;-doGeno 16:, print the posterior of the called genotype
-;-doGeno 32:, print the depth, (if availble), the number of reads used to determine the genotype llhs.
+;-doGeno 32:, somewhat different dumps the binary posts for all samples, encoded as 3*nind double
-;-doGeno 64:, somewhat different dumps the binary posts for all samples, encoded as 3*nind double
 The genotype are integers such that AA=0,AC=1,AG=2,AT=3,CC=4,CG=5,CT=6,GG=7,GT=8,TT=9